Incorrect, they had the use Rivet city's nuclear reactor to power the ship BETTER, it was being powered, and flying, just fine, before having it.

The EC BOS can certainly return, they have an established kingdom and the ability to recruit replacements.......whether they should in the face of Institute superiority is another question.

The MM and RR are of course untouchable as long as they are protected by the player, not so much without you since neither is organised to fight a resurgent BOS out for blood.